Cell Fate Determination of the Potato Shoot Apex and Stolon Tips Revealed by Single-Cell Transcriptome Analysis

Potato (Solanum tuberosum L.) is a starch-rich crop with two types of meristematic stems: the shoot and stolon. Shoots grow vertically, while stolons grow horizontally underground and produce tubers at their tips. However, transcriptional differences between shoot and stolon cells remain unclear. To address this, we performed single-cell RNA sequencing of the shoot apex and stolon tip, generating a comprehensive transcriptional landscape. We identified 23 distinct cell clusters with high cell heterogeneity, including cell-specific genes and conserved genes with cell-specific expression patterns. Hormone-related genes, particularly those involved in auxin and gibberellin pathways, exhibited distinct patterns among shoot and stolon cells. Meristematic cells were re-clustered based on the expression of StPOTH15, a homolog of SHOOT MERISTEMLESS (STM) in Arabidopsis. Co-expression networks of transcription factors identified the key transcription factors involved in stolon development. We also constructed developmental trajectories for xylem and phloem development using key vascular genes, including MP, XCP1, PP2A1 and SEOR1. Comparative analysis with Arabidopsis highlighted significant differences in cell type-specific transcript profiles. These results provide insights into the transcriptional divergence between potato shoot and stolon, and identify key transcription factors co-expressed with StPOTH15 that can be used to explore their roles in stolon development.